Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
GATA2

Cell type

Cell type Class
Prostate
Cell type
LNCAP
Primary Tissue
Prostate
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
LNCap_siSox9_D_GATA2
cell line
LNCap
chip antibody
Anti-GATA2
vendor
Santa Cruz
sirna
siSox9 (Horizon Discovery, Catalog ID:L-021507-00-0020)
treatment
DHT

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq, cells were crosslinked with 1% formaldehyde for 10 min on horizontal rotator at room temperature and cell pellets were collected and subjected to sonication. The sheared chromatin was then diluted and immunoprecipitated with 4 µg of specific antibodies at 4°C overnight. After washing, chromatin complexes were eluted with elution buffer and crosslinking was reversed at 65°C overnight. DNA fragments were purified with the QIAquick PCR purification kit. For ATAC-seq, 50,000 cells were resuspended in cold ATAC-seq resuspension buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2). Cell nuclei were then prepared by incubation in 50 μl of ATAC-seq resuspendsion buffer containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin on ice for 3 min. After centrifugation, nuclei were resuspended in 50 μl of transposition mix (25 μl 2× TD buffer ,2.5 μl Nextera Tn5 transposase (Illuminar), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, and 5 μl water), and incubated at 37 °C for 30 min in a thermomixer with shaking at 1,000 rpm. Transposed fragments were then purified with a Zymo DNA Clean and Concentrator-5 Kit. All libraries showed sufficient amplification after the 5 pre-amplification cycles and quantified using the KAPA Library Quantification Kit. For ChIP-seq, cells were crosslinked with 1% formaldehyde for 10 min on horizontal rotator at room temperature and cell pellets were collected and subjected to sonication. The sheared chromatin was then diluted and immunoprecipitated with 4 µg of specific antibodies at 4°C overnight. After washing, chromatin complexes were eluted with elution buffer and crosslinking was reversed at 65°C overnight. DNA fragments were purified with the QIAquick PCR purification kit. For ATAC-seq, the library preparation was performed with Nextera DNA Library Prep Kit for Illumina following the manufacturer's instructions. The cDNA molecules were amplified by 8 cycles of PCR. Non-size selection libraries were then sequenced for using Illumina Novaseq 6000 at the Duke sequencing core. For ChIP-seq, the eluted ChIP DNA was used for library preparation with NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina according to the manufacturer's protocol. The library was amplified with 12 PCR cycles and prepared with gel-based size selection.

Sequencing Platform

instrument_model
Illumina NovaSeq 6000

hg38

Number of total reads
51971656
Reads aligned (%)
98.2
Duplicates removed (%)
70.7
Number of peaks
3129 (qval < 1E-05)

hg19

Number of total reads
51971656
Reads aligned (%)
97.2
Duplicates removed (%)
71.6
Number of peaks
3171 (qval < 1E-05)

Base call quality data from DBCLS SRA